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Old 06-20-2016, 07:36 AM   #1
mfort001
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Location: Gainesville, FL

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Default Clustering RBH hits into files by reference gene

I have performed RBH for each of five transcriptomes against a reference genome, producing five separate output files. I figured, for ease, it was best to combine these output files into one using 'cat' command. The output looks like so, e.g.,:

Code:
    Acur_1001484	1751	OFAS000562-RA-EXON01	467	1	1039	1240	1	467	264	4.00E-62	237	87.75	179	204	1	264	467	1	1240	1039	1.00E-62	237	87.75	179	204
    Apil_comp17655_c0_seq1	2446	OFAS000562-RA-EXON01	467	1	288	453	1	289	454	2.00E-66	252	93.98	156	166	1	289	454	1	288	453	1.00E-66	252	93.98	156	166
    Atri_comp16713_c0_seq1	2069	OFAS000562-RA-EXON01	467	1	1576	1754	1	467	289	5.00E-67	254	92.18	165	179	1	289	467	1	1754	1576	4.00E-67	254	92.18	165	179
    Btri_comp12490_c0_seq1	2547	OFAS000562-RA-EXON01	467	1	2069	2267	1	467	268	2.00E-66	252	89.5	179	200	1	268	467	1	2267	2069	1.00E-66	252	89.5	179	200
    Atri_comp10477_c0_seq1	2608	OFAS000604-RA-EXON01	1887	1	4	1159	1	298	1537	0	701	78.5	997	1270	1	298	1537	1	4	1159	0	701	78.54	999	1272
    Ctom_1008131	415	OFAS000604-RA-EXON01	1887	1	101	399	1	1260	959	1.00E-81	300	85.06	262	308	1	959	1260	1	399	101	4.00E-81	300	85.06	262	308
    Acur_1001075	997	OFAS000604-RA-EXON01	1887	1	469	954	1	756	1258	1.00E-125	448	83.69	431	515	1	247	650	1	16	417	1.00E-121	435	86.54	360	416
    Btri_comp18753_c0_seq1	2786	OFAS000604-RA-EXON01	1887	1	420	1181	1	761	1593	1.00E-108	392	77.03	654	849	1	297	650	1	4	336	1.00E-87	324	84.49	305	361
    Apil_comp16297_c0_seq1	1235	OFAS000628-RA-EXON01	453	1	182	553	1	372	1	4.00E-66	250	78.93	296	375	1	1	372	1	553	182	4.00E-66	250	78.93	296	375
    Atri_comp15731_c0_seq1	657	OFAS000628-RA-EXON01	453	1	131	517	1	387	1	9.00E-55	211	76.73	300	391	1	1	387	1	517	131	2.00E-54	211	76.73	300	391
    Apil_comp14961_c1_seq1	1230	OFAS000635-RA-EXON02	212	1	254	452	1	1	198	2.00E-54	211	85.93	171	199	1	1	198	1	254	452	8.00E-55	211	85.93	171	199

For a given reference gene (e.g., OFAS000562-RA-EXON01), I would now like to retrieve the query IDs and the corresponding reference gene ID and copy this data into a new text file named as the reference gene ID (e.g., OFAS000562-RA-EXON01_IDs.txt). Below are four examples of what I'm wanting in terms of output from this approach:

File 1:

Code:
   OFAS000562-RA-EXON01
    Acur_1001484
    Apil_comp17655_c0_seq1
    Atri_comp16713_c0_seq1
    Btri_comp12490_c0_seq1
File 2:

Code:
   OFAS000604-RA-EXON01
    Acur_1001075
    Btri_comp18753_c0_seq1
    Atri_comp10477_c0_seq1
    Ctom_1008131
File 3:

Code:
   OFAS000628-RA-EXON01
    Apil_comp16297_c0_seq1
    Atri_comp15731_c0_seq1
File 4:

Code:
   OFAS000635-RA-EXON02
    Apil_comp14961_c1_seq1
I don't have strong bioinformatic/scripting skills, so I appreciate any feedback on how to do this.

Last edited by mfort001; 06-20-2016 at 10:54 AM.
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Old 06-20-2016, 07:42 AM   #2
GenoMax
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For reference cross-posted: https://www.biostars.org/p/196945/
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