julianhess / igv_remote

automate IGV snapshot pipeline from single and pair gs url

igv_remote

An attempt to automate snapshot/navigate pipeline from ipython.

Usage

The basic usage should be something like -

import igv_remote

# initialize a socket 
igv_remote.connect()

# setting some params for save and view options
igv_remote.set_saveopts(img_fulldir = "/home/qing/igv_snapshots/", img_basename = "test.png" ) # must be set!
igv_remote.set_viewopts(collapse = False, squish = True, viewaspairs = True ) # optional

# to get snapshot for a single/paired location
igv_remote.load_single(gspath1, <optional gspath2>,
                       <misc position params>) # see details below

# close the socket
igv_remote.close()

The <misc position params> can be specified as chromosome and start and end positions, e.g. chromosome=12, start_pos=345729,end_pos=345789 and each of the input could be a list, e.g. chromosome=12, start_pos=[345729, 345758, 345799], end_pos=[347000, 347090, 347200] In case of list input for locations, we will take multiple screen shots for each location, resulting in multiple images named as <imagename_x.png>.

There are also misc utilities including

# generate list of tuples [(chr, start, end)] for input to igv_remote.goto
igv_remote.parse_loc(chromosome, start, end)
# load bam file
igv_remote.load(gspath, <optional gspath2>)
# send navigate command to server
igv_remote.goto(*(chr, start, end))

A sample script can be found as run.py in this repo - you need to adjust imgfullpath that works for you. A sample data frame can be found at test_df.csv where it contains some gspaths of interest.

Helpers

There are some helper function to parse firecloud workspace data from Dalmatian to your desired format in dalmatian_helper.py. get_pairs_from_ws and match_pair allows you to match tumor-normal pair for each sample_id, producing a dataframe with columns for cohort tss pid tumor and normal.

import dalmatian
ws_list = dalmatian.firecloud.api.list_workspaces().json()
mp = match_pair(get_pairs_from_wsname(re_match_wsname(ws_list)))

Please note that current implementation only works the format of "controlledAccess" data.

locate_view.py is another helper function that helps to match your callset to your interested genes and cohort.

ldict = find_view(<callset pd dataframe>,
          <dataframe from match_pair>,
          <interested gene>, # "RNF5"
          <TCGA cohort>) #optional, "BRCA"

The result will be a list of dictionary with cohort, pid,gene and position. To parse it into the structure that we can copy and paste into VM ipython console, we can call format_command from locate_view.py

format_command(ldict) # the result from `find_view`

-------------------------------------------------

igv_remote.send("new ")
igv_remote.load("gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/BRCA/DNA/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AC-A2BM-01A-11D-A21Q-09.bam","gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/BRCA/DNA/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AC-A2BM-11A-13D-A21Q-09.bam")

igv_remote.goto(6,32147809)
igv_remote.goto(6,32147865)
-------------------------------------------------

igv_remote.send("new ")
igv_remote.load("gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/BRCA/DNA/WXS/UCSC/ILLUMINA/TCGA_MC3.f8dd9e14-dfa2-490e-bc37-61b6f680289f.bam","gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/BRCA/DNA/WXS/UCSC/ILLUMINA/TCGA_MC3.f35e7064-c207-4ac9-8a17-973e6f90d878.bam")

igv_remote.goto(6,32147865)
-------------------------------------------------

TODO

Try to navigate and snapshot on local machine by ssh -L

Troubleshooting

• if something like (Errno 111] Connection refused try to check if your IGV session is live or not.
• in case of [Errno 32] *Broken pipe* try to restart IGV
• imgfullpath must be full absolute path, something like "/home/hurrialice/snapshots" and you need to make sure it exists!
• try run batch job directly on IGV for debug could be helpful