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aghozlaneaghozlane
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Strain issues (#111)
* Add bcftools sort step * For now, no reference build * Update of catalogues with kegg114 and removal of the bed files.
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‎meteor/data/zenodo.json‎

Lines changed: 41 additions & 41 deletions
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@@ -1,142 +1,142 @@
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{
22
"fc_1_3_gut": {
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"file_info": {
4-
"catalogue": "https://zenodo.org/records/14181283/files/fc_1_3_gut.tar.xz",
4+
"catalogue": "https://zenodo.org/records/16982752/files/fc_1_3_gut.tar.xz",
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"filename": "fc_1_3_gut.tar.xz",
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"reference_date": "2024-11-18",
7-
"md5": "7d49c3a0e565e3e74a2e6bb67886d4c2"
7+
"md5": "98d1614334f2723fdccb94a7564efcec"
88
},
99
"taxonomy_info": {
10-
"catalogue": "https://zenodo.org/records/14181283/files/fc_1_3_gut_taxo.tar.xz",
10+
"catalogue": "https://zenodo.org/records/16982752/files/fc_1_3_gut_taxo.tar.xz",
1111
"filename": "fc_1_3_gut_taxo.tar.xz",
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"reference_date": "2024-11-18",
13-
"md5": "50942ab4f4f0aae43d7f3dd19df041d8"
13+
"md5": "eb313e2fa5f12b6953c2374949ac8c05"
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}
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},
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"gg_13_6_caecal": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14181300/files/gg_13_6_caecal.tar.xz",
18+
"catalogue": "https://zenodo.org/records/16982807/files/gg_13_6_caecal.tar.xz",
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"filename": "gg_13_6_caecal.tar.xz",
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"reference_date": "2024-11-18",
21-
"md5": "8e35a94d01aaded8fb322b7e22e0441f"
21+
"md5": "f40e4a6f70d51f11807a2ae2616ae24b"
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},
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"taxonomy_info": {
24-
"catalogue": "https://zenodo.org/records/14181300/files/gg_13_6_caecal_taxo.tar.xz",
24+
"catalogue": "https://zenodo.org/records/16982807/files/gg_13_6_caecal_taxo.tar.xz",
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"filename": "gg_13_6_caecal_taxo.tar.xz",
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"reference_date": "2024-11-18",
27-
"md5": "10b2e0e208cba88e4b635f5a317f94a2"
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"md5": "263e266a18888c28b84c364c2f5793c5"
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}
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},
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"clf_1_0_gut": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14180833/files/clf_1_0_gut.tar.xz",
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"catalogue": "https://zenodo.org/records/16982647/files/clf_1_0_gut.tar.xz",
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"filename": "clf_1_0_gut.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "e3a0b9c30461f2d478c77be7c3cdc529"
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"md5": "b6ea27061a738c761b65524785c9f2d5"
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},
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"taxonomy_info": {
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"catalogue": "https://zenodo.org/records/14180833/files/clf_1_0_gut_taxo.tar.xz",
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"catalogue": "https://zenodo.org/records/16982647/files/clf_1_0_gut_taxo.tar.xz",
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"filename": "clf_1_0_gut_taxo.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "8b1b709c741eed98ccc0c5fcdfa299ab"
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"md5": "0edddd2a44b47e211cdbf032e31f1600"
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}
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},
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"hs_10_4_gut": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14181329/files/hs_10_4_gut.tar.xz",
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"catalogue": "https://zenodo.org/records/16982835/files/hs_10_4_gut.tar.xz",
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"filename": "hs_10_4_gut.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "dd295f2ac27d68389a4a7ebc8f5b4125"
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"md5": "9a6655b80c2fe9df91241037ca8c8788"
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},
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"taxonomy_info": {
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"catalogue": "https://zenodo.org/records/14181329/files/hs_10_4_gut_taxo.tar.xz",
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"catalogue": "https://zenodo.org/records/16982835/files/hs_10_4_gut_taxo.tar.xz",
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"filename": "hs_10_4_gut_taxo.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "730b62479d835af5b217f0d9eda4ce2d"
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"md5": "5513514d0123b3580b5b7a35b61ca65e"
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}
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},
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"hs_8_4_oral": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14181351/files/hs_8_4_oral.tar.xz",
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"catalogue": "https://zenodo.org/records/16983006/files/hs_8_4_oral.tar.xz",
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"filename": "hs_8_4_oral.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "5b4d832b226c69766e6b35be229a9aa4"
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"md5": "8b4ac6627fbe382a05a9c9a24adea158"
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},
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"taxonomy_info": {
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"catalogue": "https://zenodo.org/records/14181351/files/hs_8_4_oral_taxo.tar.xz",
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"catalogue": "https://zenodo.org/records/16983006/files/hs_8_4_oral_taxo.tar.xz",
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"filename": "hs_8_4_oral_taxo.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "10565aafc059b663cbf1f7297a56047b"
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"md5": "1028078a8cc15262bad7fac6a66329ae"
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}
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},
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"hs_2_9_skin": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14181341/files/hs_2_9_skin.tar.xz",
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"catalogue": "https://zenodo.org/records/16982908/files/hs_2_9_skin.tar.xz",
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"filename": "hs_2_9_skin.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "4860182792a44058ffa671217c71d789"
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"md5": "8891e2d14458de8e94b84f816d71ca78"
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},
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"taxonomy_info": {
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"catalogue": "https://zenodo.org/records/14181341/files/hs_2_9_skin_taxo.tar.xz",
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"catalogue": "https://zenodo.org/records/16982908/files/hs_2_9_skin_taxo.tar.xz",
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"filename": "hs_2_9_skin_taxo.tar.xz",
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"reference_date": "2024-11-18",
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"md5": "68a011b4f319b118cda9b05b637dbc19"
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"md5": "e75ccba8fa2c003d8fd3f7594a08ce8c"
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}
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},
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"mm_5_0_gut": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14184128/files/mm_5_0_gut.tar.xz",
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"catalogue": "https://zenodo.org/records/16983064/files/mm_5_0_gut.tar.xz",
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"filename": "mm_5_0_gut.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "029bd928c4d5b00462bcc12950857f54"
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"md5": "cb48dfa9964bf5557f770a0b638ed1de"
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},
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"taxonomy_info": {
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"catalogue": "https://zenodo.org/records/14184128/files/mm_5_0_gut_taxo.tar.xz",
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"catalogue": "https://zenodo.org/records/16983064/files/mm_5_0_gut_taxo.tar.xz",
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"filename": "mm_5_0_gut_taxo.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "cd404b109553cc01cb93ead46a85b07b"
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"md5": "5b8806002d3958a4a6615e04deae9dd9"
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}
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},
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"oc_5_7_gut": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14184141/files/oc_5_7_gut.tar.xz",
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"catalogue": "https://zenodo.org/records/16983124/files/oc_5_7_gut.tar.xz",
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"filename": "oc_5_7_gut.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "071d2ac2bcb90545edc2104cc2aa6aef"
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"md5": "7d47a7b574985ba415cd8ece80f05004"
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},
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"taxonomy_info": {
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"catalogue": "https://zenodo.org/records/14184141/files/oc_5_7_gut_taxo.tar.xz",
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"catalogue": "https://zenodo.org/records/16983124/files/oc_5_7_gut_taxo.tar.xz",
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"filename": "oc_5_7_gut_taxo.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "f2fea0c805acc7f527e32bacfc93d59a"
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"md5": "fd0d8e193d7e756ca2f54e0b5f8baf44"
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}
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},
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"rn_5_9_gut": {
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"file_info": {
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"catalogue": "https://zenodo.org/records/14184150/files/rn_5_9_gut.tar.xz",
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"catalogue": "https://zenodo.org/records/16983154/files/rn_5_9_gut.tar.xz",
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"filename": "rn_5_9_gut.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "6b860f2ca7826a5f8473c30337635cd2"
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"md5": "f6b98fb58b163e7b9da8643db337c21f"
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},
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"taxonomy_info": {
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"catalogue": "https://zenodo.org/records/14184150/files/rn_5_9_gut_taxo.tar.xz",
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"catalogue": "https://zenodo.org/records/16983154/files/rn_5_9_gut_taxo.tar.xz",
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"filename": "rn_5_9_gut_taxo.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "131df23bfb7758c539c012bd8726eeb5"
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"md5": "ce839246085a04020327db214cd53980"
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}
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},
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"ssc_9_3_gut": {
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"file_info": {
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"complete": "https://zenodo.org/records/14184158/files/ssc_9_3_gut.tar.xz",
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"complete": "https://zenodo.org/records/16983194/files/ssc_9_3_gut.tar.xz",
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"filename": "ssc_9_3_gut.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "9b0df528d4c74662393b4c7358f69121"
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"md5": "083c5e07dc08fb21bba5175242642113"
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},
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"taxonomy_info": {
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"taxo": "https://zenodo.org/records/14184158/files/ssc_9_3_gut_taxo.tar.xz",
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"taxo": "https://zenodo.org/records/16983194/files/ssc_9_3_gut_taxo.tar.xz",
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"filename": "ssc_9_3_gut_taxo.tar.xz",
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"reference_date": "2024-11-19",
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"md5": "8cbdb0bb7cbbdcd90981ed9d7fc4ad38"
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"md5": "b35bb36fc5871660ded123bcab5bf2c9"
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}
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},
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"mock": {
@@ -159,4 +159,4 @@
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}
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}
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}
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}
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}

‎meteor/meteor.py‎

Lines changed: 33 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -186,38 +186,39 @@ def get_arguments() -> Namespace: # pragma: no cover
186186
help="Check the md5sum of the catalogue after download.",
187187
)
188188
# Define download argument parsing
189-
reference_parser = subparsers.add_parser(
190-
"build", help="Import a custom gene catalogue"
191-
)
192-
reference_parser.add_argument(
193-
"-i",
194-
dest="input_fasta_file",
195-
type=isfile,
196-
required=True,
197-
help="Fasta file of the custom gene catalogue (gzip, bzip2 and xz compression accepted).",
198-
)
199-
reference_parser.add_argument(
200-
"-o",
201-
dest="ref_dir",
202-
type=isdir,
203-
required=True,
204-
help="Directory where the catalogue and its index are saved.",
205-
)
206-
reference_parser.add_argument(
207-
"-n",
208-
dest="ref_name",
209-
metavar="REFERENCE_NAME",
210-
type=str,
211-
required=True,
212-
help="Name of the gene catalogue (ansi-string without space).",
213-
)
214-
reference_parser.add_argument(
215-
"-t",
216-
dest="threads",
217-
default=ReferenceBuilder.DEFAULT_NUM_THREADS,
218-
type=num_threads,
219-
help="Number of threads to launch while indexing the catalogue (default: %(default)d).",
220-
)
189+
if False:
190+
reference_parser = subparsers.add_parser(
191+
"build", help="Import a custom gene catalogue"
192+
)
193+
reference_parser.add_argument(
194+
"-i",
195+
dest="input_fasta_file",
196+
type=isfile,
197+
required=True,
198+
help="Fasta file of the custom gene catalogue (gzip, bzip2 and xz compression accepted).",
199+
)
200+
reference_parser.add_argument(
201+
"-o",
202+
dest="ref_dir",
203+
type=isdir,
204+
required=True,
205+
help="Directory where the catalogue and its index are saved.",
206+
)
207+
reference_parser.add_argument(
208+
"-n",
209+
dest="ref_name",
210+
metavar="REFERENCE_NAME",
211+
type=str,
212+
required=True,
213+
help="Name of the gene catalogue (ansi-string without space).",
214+
)
215+
reference_parser.add_argument(
216+
"-t",
217+
dest="threads",
218+
default=ReferenceBuilder.DEFAULT_NUM_THREADS,
219+
type=num_threads,
220+
help="Number of threads to launch while indexing the catalogue (default: %(default)d).",
221+
)
221222
# Define fastq argument parsing
222223
fastq_parser = subparsers.add_parser(
223224
"fastq", formatter_class=RawTextHelpFormatter, help="Import fastq files"

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