Sorting command is not available

[sb5169]

Hi I am trying to use PyGLtools/intersect.py

but I keep getting the follow error: File A is not sorted. Please use pgltools sort [FILE]

the top of file A is shown below.

and I cannot find the sort or fomartbedpe command: init.py closest.pyc condense.py coverage.pyc formatTripSparse.py intersect1D.pyc pgltools_library.py subtract.pyc init.pyc closest1D.py condense.pyc expand.py formatTripSparse.pyc juicebox.py pgltools_library.pyc subtract1D.py browser.py closest1D.pyc conveRt.py expand.pyc intersect.py juicebox.pyc samTopgl.py subtract1D.pyc browser.pyc column_flip.py conveRt.pyc findLoops.py intersect.pyc merge.py samTopgl.pyc window.py closest.py column_flip.pyc coverage.py findLoops.pyc intersect1D.py merge.pyc subtract.py window.pyc

chrA startA stopA chrB startB stopB AnnotationA AnnotationB

chr1 6405000 6420000 chr1 6430000 6445000 chr1:6405000:6420000 chr1:6430000:6445000 chr1 6340000 6355000 chr1 6470000 6485000 chr1:6340000:6355000 chr1:6470000:6485000 chr1 6470000 6485000 chr1 6485000 6500000 chr1:6470000:6485000 chr1:6485000:6500000 chr1 6485000 6500000 chr1 6545000 6560000 chr1:6485000:6500000 chr1:6545000:6560000 chr1 6630000 6645000 chr1 6695000 6710000 chr1:6630000:6645000 chr1:6695000:6710000 chr1 6720000 6735000 chr1 6735000 6750000 chr1:6720000:6735000 chr1:6735000:6750000 chr1 6720000 6735000 chr1 7740000 7755000 chr1:6720000:6735000 chr1:7740000:7755000 chr1 9575000 9590000 chr1 9860000 9875000 chr1:9575000:9590000 chr1:9860000:9875000 chr1 10205000 10220000 chr1 10295000 10310000 chr1:10205000:10220000 chr1:10295000:10310000

[sb5169]

just sorted manually: sort -k1,1 -k2,2n -k3,3n -k4,4 -k5,5n -k6,6n

[billgreenwald]

Hey there,

glad you got the issue taken care of through manually sorting, but I wanted to check in to fix any outstanding issues.

Above you typed "fomartbedpe" rather than "formatbedpe". Was that a typo in your posting here?

Alternatively, the tool is set up to be run from the /sh folder, rather than running the python directly. The sort commands are written in bash rather than python.

If you go into pgltools/sh/ and run

pgltools formatbedpe [FILE]

does this work?

Thanks!

[sb5169]

Hey,

Yes that was a typo. Good to know I'll try that next time.

Thanks!

Sana B. Badri Skok & Bonneau Lab New york University Langone medical center / NYU School of Medicine 550 First Avenue, Smilow research building, room 307 New York, NY 10016 mobile. 551-221-5882 E-mail: sana.badri@nyumc.org

---

From: Bill Greenwald notifications@github.com Sent: Tuesday, December 5, 2017 2:02:01 PM To: billgreenwald/pgltools Cc: Badri, Sana; State change Subject: Re: [billgreenwald/pgltools] Sorting command is not available (#2)

Hey there,

glad you got the issue taken care of through manually sorting, but I wanted to check in to fix any outstanding issues.

Above you typed "fomartbedpe" rather than "formatbedpe". Was that a typo in your posting here?

Alternatively, the tool is set up to be run from the /sh folder, rather than running the python directly. The sort commands are written in bash rather than python.

If you go into pgltools/sh/ and run

pgltools formatbedpe [FILE]

does this work?

Thanks!

- You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_billgreenwald_pgltools_issues_2-23issuecomment-2D349406422&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=Mj6pviYiC5sdWu2k1JF-BA&m=1-Il-51K8rbDSDmcM1KUxFwtu7DdP4ISnD3-EtLbEuo&s=1UPV4a2ZrDdtlHuodsbX-eeVSR2kOs9Lj3IuIq93Ja4&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIbOGfwCtgbYCAPBU-5FegID3xWKesbQxRks5s9ZMfgaJpZM4Q2x5w&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=Mj6pviYiC5sdWu2k1JF-BA&m=1-Il-51K8rbDSDmcM1KUxFwtu7DdP4ISnD3-EtLbEuo&s=7lblTpF5aQbkoa29O1yHPMseisITExXFBkUlDeh6Lls&e=.

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.